/*
 * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package org.ncic.bioinfo.sparkseq.algorithms.walker.haplotypecaller.argcollection;

import org.ncic.bioinfo.sparkseq.algorithms.walker.haplotypecaller.model.ReferenceConfidenceMode;

/**
 * Author: wbc
 */
public class HaplotypeCallerArgumentCollection extends StandardCallerArgumentCollection {

    public boolean DEBUG;

    public boolean USE_FILTERED_READ_MAP_FOR_ANNOTATIONS = false;

    /**
     * The reference confidence mode makes it possible to emit a per-bp or summarized confidence estimate for a site being strictly homozygous-reference.
     * See http://www.broadinstitute.org/gatk/guide/article?id=2940 for more details of how this works.
     * Note that if you set -ERC GVCF, you also need to set -variant_index_type LINEAR and -variant_index_parameter 128000 (with those exact values!).
     * This requirement is a temporary workaround for an issue with index compression.
     */
    public ReferenceConfidenceMode emitReferenceConfidence = ReferenceConfidenceMode.NONE;

    @Override
    public HaplotypeCallerArgumentCollection clone() {
        return (HaplotypeCallerArgumentCollection) super.clone();
    }

}
